tbuckley/cabot-search huggingface dataset:
Abstract 5022: Atypical protein kinase C inhibitors abrogate malignant breast cancer
Authors: Nuzhat Nowshin Oishee, Khandker Mohammad Khalid, Dr. Mildred Acevedo-Duncan
Journal: Cancer Research (2023)

Abstract Breast cancer is the most common cancer type with expected cases of approximately 284,200 according to the National Cancer Institute. Atypical Protein Kinase C (aPKC) plays a significant role in many cancer types. A positive correlation between elevated PKC levels and both the invasive and chemotactic potential of human breast cancer cell lines has been suggested in in-vitro studies. In addition, the atypical protein kinase C isoforms (aPKC), PKC- and PKC- are involved in the increased proliferation of several cancer types, including breast cancer and ovarian cancer. Hence, this project focused on utilizing aPKC inhibitors, ICA-1S (5-amino-1-((1R,2S,3S,4R)-2,3-dihydroxy-4-methylcyclopentyl)-1H-imidazole-4-carboxamide and - Stat (8-hydroxy-1,3,6- naphthalenetrisulfonic acid), on two malignant breast cancer cell lines (T47D and BT549) to observe the effect on cell proliferation. To observe the effects of the aPKC inhibitors on the malignant breast cancer cells, cell proliferation assays were conducted, where cells were treated with ICA-1S, and - Stat for 72 hours (about 3 days). Furthermore, to observe if ICA-1S induces apoptosis in the malignant breast cancer cells, both the cell lines were treated with ICA-1S for 120 hours (about 5 days), and western blotting techniques were utilized. The results indicated that in T47D cell line, treatment with ICA-1S (50uM) and - Stat (10uM) caused 52% and 75% reduction in cell proliferation, respectively. Moreover, with BT549 cell line, treatment with - Stat (1uM) decreased the cell proliferation by 40%. Additionally, it was observed by western blotting that ICA-1S induces apoptosis in BT549 cell line. This was shown by an increase in the cleavage of caspase 3 and PARP, along with a decrease in survivin, and phospho-BAD. However, ICA-1S did not induce apoptosis in T47D cell line. Further investigation will be conducted on determining the effect of aPKC inhibitors on the proliferation, invasion, and migration of the malignant breast cancer cell lines. In addition, siRNA treatment will be applied to knockdown PKC- and PKC- and subsequent effect will be observed. In conclusion, PKC- and PKC- plays a significant role on breast cancer, and further investigation will be conducted to analyze these roles, which will lead to the determination of a signaling pathway via which atypical protein Kinase C functions in breast cancer. Citation Format: Nuzhat Nowshin Oishee, Khandker Mohammad Khalid, Dr. Mildred Acevedo-Duncan. Atypical protein kinase C inhibitors abrogate malignant breast cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5022.
Abstract 5310: An expanded quantitative protein expression atlas of human cancers
Authors: Han Liang
Journal: Cancer Research (2023)

Abstract The Cancer Genome Atlas (TCGA) and Cancer Cell Line Encyclopedia (CCLE) are the most widely used and deeply characterized resources for cancer research. Despite rich molecular and phenotypic data available for these cohorts, large-scale proteomic data across cancer lineages remain limited. Here we expanded our previous effort to generate high-quality protein expression data of 447 clinically relevant proteins for ~8,000 TCGA patient samples and ~900 CCLE cell line samples using reverse phase protein arrays. We show that the protein expression profiles provide deeper mechanistic insights into cancer dependency and serve as a sensitive functional readout for the fitness effect of somatic mutations, e.g., BRAF mutations. We develop a protein-centered strategy to identify synthetic lethality pairs with high confidence. We identify pro- and anti-metastasis protein markers and demonstrate their prognostic relevance in patient cohorts. Collectively, this dataset provides a valuable resource for elucidating cancer mechanisms, identifying protein biomarkers, and developing therapeutic strategies. Citation Format: Han Liang. An expanded quantitative protein expression atlas of human cancers. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5310.
Abstract 4974: Development of novel pyrimido-pyrazolo-quinolone derivative, IND-2 as multi-targeted inhibitor for the treatment of prostate cancer
Authors: Swapnaa Balaji, Rabin Neupane, Chandrabose Karthikeyan, Jayachandra Babu Ramapuram, Amit K. Tiwari
Journal: Cancer Research (2023)

Abstract Prostate cancer (PC) is the most commonly diagnosed cancer in men. In PC, multiple molecular signaling networks are perturbed, so monotherapies are less effective, creating an urgent need to discover chemotherapeutic agents that target multiple tumor-promoting proteins simultaneously. Drug discovery research is increasingly embracing poly-pharmacology, in which one drug targets multiple oncogenic targets concurrently. We have identified a novel quinoline derivative, IND-2 (4-chloro-2-methylpyrimido[1″,2″:1,5]pyrazolo[3,4-b]quinolone), that has been shown to significantly inhibit the expression of several oncogenic and epigenetic targets in PC cells. It was observed that IND-2 significantly inhibited the proliferation of PC-3 and DU-145 with IC50 values of 3 µM and 3.5 µM, respectively. Furthermore, 5 and 10 µM of IND-2 produced morphological changes in PC-3 cells characteristic of apoptosis. The levels of reactive oxygen species (ROS) increased significantly after IND-2 was added to PC cells. Additionally, 5 and 10 µM of IND-2 reduced mitochondrial membrane potential in PC-3 cells. Furthermore, IND-2 increased the expression of cleaved caspase-3, cleaved caspase-7, and cleaved poly (ADP-ribose) polymerase (PARP). The PC-3 cells incubated with 5 µM of IND-2 showed a significant reduction in expression of B-cell lymphoma 2 (Bcl-2). These data convincingly show that IND-2 inhibits PC cells through apoptosis induction. It is interesting to note that IND-2 (2.5, 5 and 10 µM) also induces mitotic catastrophe in PC-3 cells. Wound healing assay and expression of several EMT (epithelial to mesenchymal) markers indicated significant anti-metastatic activity of IND-2. Target identification studies have demonstrated that IND-2 mimics etoposide (VP-16) and binds more specifically to Topoisomerase IIβ. In our preliminary studies, we found that IND-2 inhibits several oncogenic and epigenetic targets including Topoisomerase II-Hsp90 complex and LSD1/HDAC1 of the transcriptional corepressor CoREST complex. However, these targets need to be validated to understand IND-2's mechanism. Overall, IND-2 may lead to the development of more effective poly-targeted compounds for PC treatment. Citation Format: Swapnaa Balaji, Rabin Neupane, Chandrabose Karthikeyan, Jayachandra Babu Ramapuram, Amit K. Tiwari. Development of novel pyrimido-pyrazolo-quinolone derivative, IND-2 as multi-targeted inhibitor for the treatment of prostate cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4974.
Abstract 3939: Inhibition of USP7 upregulates USP22 through desuppression of transcriptional activity of Sp1 in human cancer cells
Authors: Keqiang Zhang, Ting Sun, Wendong Li, Jun Wu, Dan Raz
Journal: Cancer Research (2023)

Abstract Deubiquitinases (DUBs) play important roles in various human cancers and targeting DUBs is considered as a novel anticancer therapeutic strategy. Overexpression of ubiquitin specific protease 7 and 22 (USP7 and USP22) are associated with malignancy, therapy resistance, and poor prognosis in many cancers. Although both DUBs are involved in the regulation of similar genes and signaling pathways, such as histone H2B monoubiquitination (H2Bub1), c-Myc, FOXP3, and P53, the interdependence of USP22 and USP7 expression has never been described. In the study, we found targeting USP7 via either siRNA-mediated knockdown or pharmaceutical inhibitors dramatically upregulates USP22 in cancer cells. Mechanistically, the elevated USP22 occurs through a transcriptional pathway, possibly due to desuppression of the transcriptional activity of SP1 via promoting its degradation upon USP7 inhibition. Importantly, the elevated USP22 leads to significant activation of downstream signal pathways including H2Bub1 and c-Myc, which may potentially enhance cancer malignancy and counteract the anticancer efficacy of USP7 inhibition. Importantly, targeting USP7 further suppresses the in vitro proliferation of USP22-knockout (USP22-Ko) A549 and H1299 lung cancer cells and induces a stronger activation of P53 tumor suppressor signaling pathway. In addition, USP22-Ko cancer cells are more sensitive to a combination of cisplatin and USP7. USP7 inhibitor treatment further suppresses the in vivo angiogenesis and growth and induced more apoptosis in USP22-Ko cancer xenografts. Taken together, our findings demonstrate that USP7 inhibition can dramatically upregulate USP22 in cancer cells; and targeting USP7 and USP22 may represent a more effective approach for targeted cancer therapy, which warrants further study. Citation Format: Keqiang Zhang, Ting Sun, Wendong Li, Jun Wu, Dan Raz. Inhibition of USP7 upregulates USP22 through desuppression of transcriptional activity of Sp1 in human cancer cells. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3939.
Abstract 5309: Isolation and validation of small extracellular vesicles from rhabdomyosarcoma cells
Authors: Paula R. Quaglietta, Ashby Kissoondoyal, Ethan Malkin, Salvador Mejia, Ann Gong, David Malkin, Reto M. Baertschiger
Journal: Cancer Research (2023)

Abstract Extracellular vesicles (EVs) are nano-sized (30-1000 nm) membranous particles released by nearly all cell types. EV biology is a rapidly growing field, however its relative novelty and the intrinsic heterogeneity of EVs result in a lack of standardized and reproducible protocols. We sought to develop and validate an EV isolation method using rhabdomyosarcoma cell lines, with multiple characterization/validation methods, to improve the reproducibility and reliability of EV research in pediatric cancer research. EVs were isolated and analyzed in triplicate from 4 rhabdomyosarcoma cell lines (RH4, RH18, RH30, RD), of varying clinical characteristics including subtype, TP53 status and FOXO1 fusion status. Cells were grown to 70% confluency in six 175cm2 flasks, to ensure sufficient EV content for all downstream analyses, then incubated for 48 hours in media containing 10% EV-depleted FBS. The resultant 120mL of conditioned media (CM) per cell line was collected and subject to differential ultracentrifugation to isolate EVs. CM was centrifuged twice, then concentrated to less than 10mL using 3kDa MWCO filter tubes. Concentrated CM was centrifuged twice before passing through a 0.22μm pore-sized syringe filter prior to the final ultracentrifugations. The sample was ultracentrifuged and the EV pellet was carefully washed, re-centrifuged and resuspended in 100μL of PBS. Protein analysis by Western blot confirmed the presence of EV markers (syntenin-1, TSG101) and absence of non-EV markers (calnexin, histone H2Ax). EV quantification and size distributions were evaluated by NanoSight nanoparticle tracking analysis and visualized by transmission electron microscopy. All isolations were positive for EV markers and negative for non-EV markers by Western Blotting. All isolations showed similar size distributions by nanoparticle tracking analysis, within the range of 30-250nm. EVs in each sample with the typical cup-like shape were observed in electron microscope images of EVs. Overall, our method demonstrates good reproducibility of EV isolations from multiple rhabdomyosarcoma cell lines. This methodology can be used as a baseline for other cell lines to provide greater consensus within the field, allowing further discoveries analyzing the secretome of patient-derived cell lines with the potential to translate into more specific diagnostic tools. Citation Format: Paula R. Quaglietta, Ashby Kissoondoyal, Ethan Malkin, Salvador Mejia, Ann Gong, David Malkin, Reto M. Baertschiger. Isolation and validation of small extracellular vesicles from rhabdomyosarcoma cells. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5309.
Abstract 6209: O6-methylguanine as the junction of MGMT and PARP1-mediated repair pathways
Authors: Jodie D. Cropper, Dauren S. Alimbetov, Kevin T. Brown, Andrew Robles, Rostislav I. Likhotvorik, James T. Guerra, Yidong Chen, Youngho Kwon, Raushan T. Kurmasheva
Journal: Cancer Research (2023)

Abstract Temozolomide is the first-choice DNA alkylating agent and has been commonly used in oncology over the last several decades. The cytotoxicity that temozolomide elicits through the methylation of guanine and adenine residues often becomes the limiting factor in effective treatment. Despite growing evidence of dysregulated alkylating DNA damage repair as a driving force of genome instability leading to cancer, neurological diseases, and premature aging, little is currently known about the coordinated role of PARP1 and MGMT (O6-methylguanine methyltransferase) enzymes in the repair of temozolomide-induced methylated DNA lesions. A major PARP1 function in DNA damage is facilitation of repair of the methylated DNA lesions, N6-methyladenine and N7-methylguanine, via base excision repair (BER); while MGMT restores guanine in O6-methylguanine (O6meG), the most cytotoxic adduct, by a one-step catalysis. It is generally thought that BER and MGMT represent two distinct mechanisms for removing DNA damage induced by alkylating agents; however, using a number of advanced cell-free and cell-based approaches, we provided evidence for direct (DNA-independent) and indirect (through PARylation) interaction between PARP1 and MGMT and demonstrated a functional crosstalk between these repair pathways. Particularly, O6meG repair activity is increased once PARP1 PARylates MGMT. Further, longer (more clinically relevant) exposure to temozolomide induced stronger MGMT PARylation in cells, indicating that the PARP1-MGMT interaction is important for enhanced O6meG repair and cell survival. As PARP1-MGMT complex forms in a variety of cancer cell types, our findings have strong implications for the development of an effective cancer therapy for cells dependent on PARP1 and MGMT mediated DNA repair. Citation Format: Jodie D. Cropper, Dauren S. Alimbetov, Kevin T. Brown, Andrew Robles, Rostislav I. Likhotvorik, James T. Guerra, Yidong Chen, Youngho Kwon, Raushan T. Kurmasheva. O6-methylguanine as the junction of MGMT and PARP1-mediated repair pathways. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6209.
Abstract 6155: Lurbinectedin exhibits combinatorial activity with BCL2/BCL2L1 inhibitors <i>in vitro</i> and <i>in vivo</i> by modulation of MCL1 expression
Authors: Kedar S. Vaidya, Aparna Gupta, Robert Hauptschein, Robin C. Humphreys
Journal: Cancer Research (2023)

Abstract Lurbinectedin (Zepzelca) is a marine-derived anti-tumor agent currently approved for metastatic small cell lung cancer (SCLC). Lurbinectedin has been previously shown to exert its anti-tumor effect by binding to the minor groove of DNA and inhibition of nucleotide excision repair. In addition, lurbinectedin inhibits transcription by inducing degradation of RNA polymerase II. While these activities hint towards a general mechanism, specific molecular targets for lurbinectedin remain obscure. We demonstrate that in vitro, Lurbinectedin specifically induced downregulation of MCL1 protein, a member of the BCL2 family of pro-survival proteins, in a dose- (0-30 nM) and time-dependent manner (0-24 h) by Western analysis. Expression of other pro-survival proteins BCL2 and BCL2L1 were not affected. The downregulation of MCL1 was consistent in all nine tumor cell lines tested regardless of indication. Increased activity or expression of MCL1 is a known compensatory mechanism to offset loss of BCL2 or BCL2L1. We therefore hypothesized that lurbinectedin induced MCL1 loss, along with inhibition of the pro-survival proteins BCL2 and BCL2L1 would lead to an enhancement in cell killing. Consistent with the dominant pro-survival role of BCL2 in SCLC, the combination of lurbinectedin with a specific BCL2 inhibitor (venetoclax) in vitro induced synergistic cytotoxicity (measured by Bliss Sum analysis) in a panel of small cell lung cancer lines. In solid tumor lines other than SCLC, the combination of lurbinectedin with a specific BCL2L1 inhibitor (A-1331852) was also synergistic. Correspondingly in vivo, enhancement in the efficacy of lurbinectedin was observed in combination with venetoclax in SCLC models, while in solid tumor models other than SCLC the combination with a specific BCL2L1 inhibitor enhanced efficacy. Collectively, these data identify MCL1 as a specific lurbinectedin target and suggest that combinations that target other pro-survival proteins may represent a viable strategy to enhance the anti-tumor activity of lurbinectedin. Citation Format: Kedar S. Vaidya, Aparna Gupta, Robert Hauptschein, Robin C. Humphreys. Lurbinectedin exhibits combinatorial activity with BCL2/BCL2L1 inhibitors in vitro and in vivo by modulation of MCL1 expression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6155.
Abstract 6222: Clinical impact of p53 and AXL immunostaining on the efficacy of immune checkpoint inhibitor-based therapy after osimertinib treatment in patients with epidermal growth factor mutant non-small cell lung cancer
Authors: Kenji Morimoto, Tadaaki Yamada, Shinsaku Tokuda, Koichi Takayama
Journal: Cancer Research (2023)

Abstract Background: Current evidence indicates that immune checkpoint inhibitors (ICIs) have a limited efficacy in patients with lung cancer harboring epidermal growth factor receptor (EGFR) mutations. However, there is a lack of data on the efficacy of ICIs after osimertinib treatment, and the predictors of ICI efficacy are unclear. Methods: We retrospectively assessed consecutive patients with EGFR-mutant NSCLC who received ICI-based therapy after osimertinib treatment at 10 institutions in Japan, between March 2016 and March 2021. Immunohistochemical staining was used to evaluate the expression of p53 and AXL. The deletions of exon 19 and the exon 21 L858R point mutation in EGFR were defined as common mutations; other mutations were defined as uncommon mutations. Results: A total of 36 patients with advanced or recurrent EGFR-mutant NSCLC were analyzed. In multivariate analysis, p53 expression in tumors was an independent predictor of PFS after ICI-based therapy (p = 0.002). In patients with common EGFR mutations, high AXL expression was a predictor of shorter PFS and overall survival after ICI-based therapy (log-rank test; p = 0.04 and p = 0.02, respectively). Conclusion: The levels of p53 in pretreatment tumors may be a predictor of ICI-based therapy outcomes in patients with EGFR-mutant NSCLC after osimertinib treatment. High levels of AXL in tumors may also be a predictor of ICI-based therapy outcomes, specifically for patients with common EGFR mutations. Further prospective large-scale investigations on the predictors of ICI efficacy following osimertinib treatment are warranted. Citation Format: Kenji Morimoto, Tadaaki Yamada, Shinsaku Tokuda, Koichi Takayama. Clinical impact of p53 and AXL immunostaining on the efficacy of immune checkpoint inhibitor-based therapy after osimertinib treatment in patients with epidermal growth factor mutant non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6222.
Abstract 1237: Zeb1-mediated autophagy enhances resistance of breast cancer cells to genotoxic drugs
Authors: Nick A. Barlev, Olga Fedorova, Alexandra Daks, Eugene M. Tulchinsky
Journal: Cancer Research (2023)

Abstract This report presents novel results on the involvement of epithelial to mesenchymal transition (EMT) in the process of autophagy. Autophagy is a highly conserved process of cellular self-digestion that involves the formation of autophagosomes for the delivery of intracellular components and dysfunctional organelles to lysosomes. This process is induced by different signals including starvation, mitochondrial dysfunction, and DNA damage. The molecular link between autophagy and DNA damage is not well understood yet. Importantly, tumor cells utilize the mechanism of autophagy to cope with genotoxic anti-cancer drug therapy. Another mechanism of drug resistance is provided to cancer cells via the execution of the EMT program. One of the critical transcription factors of EMT is Zeb1. Here we demonstrate that Zeb1 is involved in the regulation of autophagy in several breast cancer cell models. On the molecular level, forced expression of Zeb1 in otherwise epithelial cells likely facilitates autophagy through the regulation of several autophagic genes, resulting in increased LC3-II levels, augmented staining with Lysotracker, and increased resistance to genotoxic drugs. On the contrary, the attenuation of Zeb1 expression in TNBC cells led to the opposite effect. Consequently, we propose that Zeb1 augments the resistance of breast cancer cells to genotoxic drugs, at least partially, by promoting autophagy. Collectively, we have uncovered a novel function of Zeb1 in the regulation of autophagy in breast cancer cells. Citation Format: Nick A. Barlev, Olga Fedorova, Alexandra Daks, Eugene M. Tulchinsky. Zeb1-mediated autophagy enhances resistance of breast cancer cells to genotoxic drugs [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1237.